In the Aftermath
by Us-And-Them
Summary: Post-Revolutions. Everything has repercussions. Smith is brought into the real world for a proper execution.
1. Initium

**A/N: **I must have written about a thousand outlines for this thing, and I've still never bothered to finish it. *insert self-deprecating comments* At any rate, here are a few things worth noting:

1) This is set three months after the end of Revolutions, in an universe where Neo was resuscitated in 01, and Smith's programming wasn't quite erased. The movie ending was ambiguous(ish), but I'm going to call this one and say the Wachowskis killed them off for good, so in that sense this story is an AU. That said, I've tried to write it so that it could theoretically follow the trilogy with no explicit changes to canon. Anything inconsistent is a mistake on my part.

2) Someone mentioned Neo's eyesight in a review a while back, and yes, Neo can see. That will be explained eventually (I hope), but for the moment I'm working off the principle that if the machines can do something about the viscera-liquefying electric shock Neo recieved at the end of Revolutions, they can repair and/or replace human eyes. Whether they would is another question, since blindness is non-life-threatening, but I think they'd be a little unnerved by Neo's ability to see the Source without interference in the Real World, and would probably take the opportunity to rid him of it while still technically doing him a favor.

3) A lot happens over the course of the trilogy. Neo gets more confident/competent/responsible/etc, but he also, ironically, loses a lot of his ability to connect with the human race. I think Trinity represented the last of that for him, and while it's pretty obvious how intense his grief for her is, I feel like the repercussions of her death would extend much farther than that. I'm not trying to write him exactly the way I see him in the movies, as I don't think he really would be anymore. But again, I make mistakes, and if anything about the portrayal seems unrealistic or way out of character please say so. The same goes for Smith and the others. Comments are more than appreciated.

* * *

**Initium, -i **_**n**_**: entrance, beginning**

It's silent.

If they could be honest with themselves they'd say it's the silence that makes it intolerable. There are four men on deck and none speaking. Their movements are all tamped down. The engines are too loud with no one there drowning them out.

It goes like this: The captain is tired. The commander is sullen and they're clashing. The operator hasn't left the monitor in hours and the mechanic is hiding below deck. The lieutenant—and he'd never get used to the title—is standing a ways to the side, dreading the moment when the tension finds air to start burning. The place is pin-drop silent, he's thinking, and they can't afford this. If they aren't careful, the whole room will go up in flames.

*

It's been weeks since the message. Three and a half, to come down to specifics, and more than one person is counting. 01 was brief, and that was normal, no extra information, no addendums, just a transmission requesting immediate counsel. They asked for the One specifically—the Anomaly, as they would probably always call him—and that was _not _normal. They had ways of sounding urgent in only a few words. Asking for Neo was, undeniably, one of those ways. Demanding him 'immediately' was another. Zion responded immediately.

The Council sent Morpheus to accompany him, and the military sector sent Locke. Two days later, the three met the Machines' envoys out in the tunnels, at a neutral point between the cities. The location had been set for some time. It was not rare for them to use it. A good three months into the peace, this sort of negotiation could almost be considered routine. It was the tone that kept Zion off-kilter. The request for _Neo_ and not _an ambassador._ There was talk of traps and betrayal amongst the public, but after one hundred years, the Council felt certain it could recognize hostility. 01's transmission did not feel like a threat against Zion or her people. It felt like a distress call.

If Neo read anything more into the message than they did, he never said so. And he himself could not be certain that he really knew. He berated himself for paranoia in those first few days. He was as surprised as anyone else when the other shoe came down on them, and no one could deny that. But, if pressed, he'd have had to admit he had guessed _something_ well before all the commotion. The program called 'Smith' had not died, he was sure, and they were bound to hear from him eventually.

There were reasons for him to suspect it—the Oracle's words to him, for one thing, words like _opposite_, and _negative_, and_ balance_. Her words were to be taken with a grain of salt, but he'd felt it too—that vague, amorphous sensation. Who was to say either one of them would ever really be gone for good? Neo himself had been resuscitated by the Machines only a few hours after the end, and even then he'd felt something, far from his mind as it had been at the time, shivering on a platform in the dark. He'd always been able to tell. And, guiltily, he'd have to say a part of him knew this was coming. He'd hoped it wouldn't. He'd hoped—maybe—that one day the feeling would take care of itself, that the neglect would make it disappear, and he'd never have to believe that it was real, or valid, or _there_. He'd just know, then, that Smith had been deleted and it was over. Maybe. He's not sure.

It never happened. The System, the envoys informed them, had been attempting to delete Smith for months. And failing. No one was quite sure what went wrong. They'd been keeping him in a separate construct, sealed off from the Matrix. It was impenetrable. They'd had perfect control. But even rewriting their purge program had earned them very little progress. It was possible, they said, that Smith's code had become so entangled with the system that deleting him now would be impossible. It would be like destroying a cockroach. And after four successive tries, no one's really willing to risk doubting that anymore. They've all been well-versed in the consequences of wasting too much time.

*

"_But what do you need us for?"_

_The red eyes shifted to face him, two lights in a metal skull. He supposed it was meant to look human. The similarities never failed to unnerve him. "The Virus must be removed from the system at all costs."_

_Neo stared down at the tabletop, breaking the beginnings of eye contact, or something very much like it. The machine looked distressed—if it were possible for a machine to even feel something so basic and visceral._

"_You are aware that it is possible to download a program's consciousness into the physical world?" _

_There was a pause long enough for Neo to confirm that before it went on. _

"_If deletion of the Virus is impossible within the system, it was thought that its destruction could be completed outside of the Matrix." Another pause. "But a droid in the physical world necessarily possesses a heightened connection to the Source."_

_Neo nodded, finishing the thought, "And that would be too dangerous."_

"_Precisely."_

"_But then what do you…?" He trailed off and the machine almost seemed to squirm. Is it nervous? Can they get nervous?_

"_The process has never been attempted with a human vessel…."_

*

The body that is to be Smith's is strapped to the jack-in chair, restrained as much as they could manage, Morpheus and Locke on either side, waiting. They're all waiting.

Link is sitting at the monitors, conducting what may be the most complex hack of his life as he wades through encryption. The others are engaged in pointed silence. Neo is standing by the wall, watching, telling himself he's standing guard because they may need him before the end.

They are three days out of Zion. They'd taken one to reach broadcast depth, and another to set up the equipment. The crew was kept small—only the four of them on deck, and a novice mechanic along for ship maintenance. They have orders to stay out for three weeks before coming home, all the while holding Smith as their captive on board. In that time 01 will run scans through the system, assure themselves that bringing Smith into the Real World will serve its purpose. No one wants to see him come back, least of all after this. His execution is left in limbo until they know. They are exactly on schedule.

*

_Neo could feel his mouth go dry. Yes, it had been attempted. Yes, it would work. Of course it would work._

_It was partly his fault. He'd never made it public. When it really came down to it, no one in either city knew what had gone on once the Logos left the Hammer that last night. They had what was necessary, what they'd seen and been told of in fragments—the wreck of the ship, Trinity's death, Neo's bargain—the abrupt and violent end of a very long war. They knew the basics. They knew the end result._

_But the specifics were something Neo had kept to himself. He'd been in no condition to explain when he first returned to Zion, and even later, when others pressed for information, he'd only say what they needed to know. That much was difficult enough. They didn't need the rest. No one knew exactly how the ship had reached the city or how it had crashed. No one knew the details of Trinity dying in the wreckage, how seriously they'd been attacked or that Neo had been blind._

_And no one knew about Bane._

_For all intents and purposes, Bane was a madman suffering from the effects of VDTs. He'd stowed away on the Logos, caused a brief struggle, and then it was over. That was all there was to say. Neo had not corrected the assumption. To give the rest would be to relive every moment that Smith had held a knife to Trinity's throat, to remember having his eyes cauterized by a metal coil, to remember the feeling of being unable to see the woman he loved in the last few seconds she was alive. He recounted it to no one. At times he felt he should have explained—at least for the sake of clearing Bane's name—but he never told them. And, after a while, no one asked._

_And now, once again, it was back to being real, an unpleasant fact and not a bad dream born of post-traumatic stress and long nights, and Neo debated for a moment whether he needed to say it. Whether he could even open his mouth. The room was waiting for his answer and he couldn't seem to break the silence. _

_He was spared the effort. "Bring that thing here? Onto one of our ships? Are you insane?" The two envoys turned to see Locke, clenching the edge of the table and glaring._

"_We see no other alternative."_

"_No." Neo's own voice was hoarse, barely audible. "You can't do that."_

*

He didn't tell them, didn't mention Bane. Even then, he wasn't willing to touch that last resort. But he did as best he could to persuade them without it. It wasn't about the danger. In spite of everyone's gut reaction, the ordeal wouldn't pose much of a threat. It would last twenty-one days—thirty at most—during which time Smith would be kept in a cell, under lock and key, in a ship a good twenty miles from Zion, and with no more physical power than a human shell could offer him, there was only so much he could do from a cell. Once the Machines had finished scanning the Matrix and were satisfied that he was no longer there, the crew would execute him in the Real World, and that would be the end of it. Twenty-one days was five hundred hours, was thirty thousand minutes, was two million seconds. It would be quick. No one would be hurt.

But what they were planning had crossed the line from execution into something like murder. Killing in the Matrix had been one thing. It was necessary. One had to adapt. They'd been at war. And Neo had seen Smith die before. They were both damned, it seemed, to a series of trivial deaths at each others' hands. He'd killed him again—and again—and it had all mattered so little so long as the war could be brought to an end, so long as the human race could go on living. It has a different cast to it in peacetime. This will be so much longer, so much more drawn out and humiliating. The urgency is gone. He doesn't feel right without it.

Smith hated him. Neo was always aware of that. But it was a sentiment he'd never quite managed to return. He'd disliked him, wished him dead for all the right reasons. He'd been angry with him, and—far enough back—a little afraid of him, but that doesn't amount to hatred. Hate takes energy, devotion, and there had been more important things during the war. There had been Zion and the prophecy. There had been Trinity. Smith had never been the only enemy. His death was not the goal. And Neo had felt very little towards him. It was only there, in that room, that he'd found himself wishing he had some hatred to justify what they'd do—he'd wanted so badly to argue. By the end of the meeting he was grasping at straws.

He reminded himself who this was—_what_ this was—and it was easier. He closed his eyes when the decision was made. There would always be choices like these. He would never get used to them.

*

"_You don't want to do this either."_

"_For the sake of the treaty, it must be done." Morpheus's tone was off as he spoke, straining with forced assurance and calm. Neo watched him from across the room, shot him a look that said _'I know you don't believe that'_ and kept silent. Morpheus was pacing. Neo was leaning against the far wall with his head down, staring at the floor. They were alone. Time passed and no one spoke._

_After ten minutes of nothing, Morpheus stopped at the door and turned. "The ship leaves tomorrow."_

*

"Alright, sir, I think I got it. But this is gonna be messy." Link shoots a glance back at the captain and he nods.

"Go ahead, Link." And there is the strain, again, in his voice. Neo wonders if he was the only one to notice, if Morpheus even noticed himself. Link's keystrokes slow down as he approaches the end of the sequence. Neo follows the code for a moment with his eyes. Five seconds to go. The others are watching it too. Every five minutes for the past half hour, someone's looked back at that screen. Link hesitates a moment and hits another key, turning back towards the deck with a tense little smile. Another moment passes.

"Here we go."


	2. Suscitatio

**Suscitatio, -ionis **_**f**_**: rekindling, awakening**

_Here we go_.

Neo takes a step or two backwards, one more foot away from the center of the deck. It brings him out of view, into the shadows. It may simplify things.

The code on the screen is shifting. It's been in flux for hours, but it's picking up speed and, on that cue, Smith's body gives a jerk. Neo looks away, fixing his eyes to a spot on the floor. It _looks_ like Smith—the body. 01's technology is past comparison. It was via a variant of cloning that they'd managed to create the shell. They'd needed a blueprint. What better blueprint than Smith himself? And to see it, strapped to the chair—that lifeless thing is going to be Smith, and is going to be conscious, and is going to be _here_. Neo checks his position again and begins counting in his head. _Ten…nine…eight…_

Another shift, and the screen is bizarre to watch. The language is a novelty on its own, altered symbols, subtle changes that make the familiar code oddly difficult to read. The Machines told them little about it—it wasn't necessary information—and Neo finds himself wondering exactly what it had been. A room? A cell? A white expanse? The bits of code he can catch don't offer him much. It feels like watching a moving cryptogram where all the letters are present but flipped around and turned upside down on their heads. The only thing he can make out of the mess are the moments when it—

—shifts. It was a prison and it has no exit. It hadn't been programmed with one. It existed solely to keep Smith contained, and practical as that may have been, they've found themselves hacking a system on lockdown. Even with the help of the Machines, gaining access was a five-hour process, and—having witnessed this all start to finish—there's the common notion on board the ship that they may wind up deconstructing their prisoner here and now. "Messy" was anything but an overstatement.

There's a brief glitch on the screen and the room tenses, but it takes another moment, an interminable and silent one, for anything else to start up. Neo winces when he hears Smith scream. Only in the most technical sense could that be taken for a good sign.

_Three…two…one._ The screams cut off and he looks up, over at the screen—not at Smith but at the screen. They do, at least, know it worked. The code has returned to normal.

*

"_You know, it was supposed to be my shift an hour ago."_

_Neo answered him without turning, keeping his eyes on the steady flow of symbols dripping down the console. "Sorry." The time was floating just beyond two AM. "I couldn't sleep. Figured I could take another one."_

_He could feel Link giving the back of his head a look of vague concern. It wasn't necessary—he wanted to tell him that it wasn't necessary. Several months ago the world had come to an end. That was what they were afraid of, what they thought he was thinking. But the world was still spinning, seconds still passed, gravity had not shut itself off and left them to drift into space. Sleep had never been easy for him, even when he'd had her, and he could never put words to this. Not adequately, no matter how often his friends made it clear they wanted to ask. There was nothing else for him to say. He missed her. And he'd never been good with words._

_He clicked a few keys and switched the view on the screens, routinely—mechanically. Link was still standing a foot or two behind him. After a moment, Neo turned around._

"_I've got this one," he gestured to a tin mug, smiling faintly, "…I've got coffee and everything."_

_The look didn't quite go away. "Alright, well, you're gonna owe me tomorrow. I'm taking that shift of yours, no arguments."_

_He was trying to make him laugh. And Neo did, falling silent only after Link had turned and faded back into the hallway. The door closed and the deck was quiet again. He went back to the screens and felt flat._

*

Neo had decided, some time ago, that it was one thing to kill somebody. It doesn't have to be painful, it doesn't have to be cruel, and sometimes, really, the proverbial 'other options' just aren't there to make life easier. He's learned how to that much. But this is unlike any other encounter, and he has never, in his life, never learned how to witness somebody in pain. He could never have expected to see Smith look so—terrified. He's hyperventilating. There are already red marks appearing on his wrists from where he's pulling at the restraints. For several seconds he doesn't appear to have recognized any of them, to really be seeing the room at all, and Neo finds himself staring back at the floor. A part of him had been worried he'd enjoy this, enjoy watching it. He isn't. They'd always been invulnerable in the Matrix. The display is unnerving at best.

It's Locke who finally speaks up. And it's numbing, even from the outside, the impatient and military tone he takes on, the way he seems so unruffled when the rest of them could have been sick. He is every bit the flinty commander of Zion at that moment. "You're probably wondering where you are."

Smith's eyes seem to focus for the first time and he looks up at Locke with the barest beginnings of a glare. Neo watches him—knowing Smith will recognize this place in a moment, wary of his reaction when he does—fully expecting the disgust and the rage he remembers from Bane in those twenty minutes on the deck of the Logos. He waits for him to come back to himself, coolly snap through the restraints and take Locke by the throat, and as ridiculous as the thought is, the biggest surprise is when nothing happens at all. Neo notes then, only then, that Smith is barely remaining conscious.

_*_

_"I don't trust him…" Neo paused, avoiding the eyes of the Council and the captains as he worked through his response, "But I don't think 01 is lying. They have no reason to lie."_

_"Is it your opinion, then, that 'Smith' would not return to the Machines as an agent, even under these circumstances?"_

_Morpheus broke in, "Counselor, 01 has disabled nearly all of its agents since the treaty was passed. With all due respect, I do not believe there are any grounds on which to suspect a conspiracy."_

_"True, but you must admit, Captain, their request is rather strange." Haman had his gaze fixed passively on Neo from his seat behind the table. "I think I'd like to hear what your Lieutenant has to say on the matter."_

_Neo kept his eyes on the ground. He was careful with his words, careful not to stumble over them. He had never been comfortable with this, with people, with crowds, and before the Council every little thing was a matter of importance. He didn't like to be reminded how many people were tuned into every word he said, or how much his opinion could matter. It had gotten worse since the end of the war. So many of them now just expected him to know. Everything. No one doubted him anymore._

_"Thank you, Counselor." And it was terrifying. "Smith wouldn't go back to the System. Not- not willingly. If the Machines wanted to infiltrate a ship, they wouldn't do it like this. Smith is—not reliable." And, of course, what he'd wanted to say is 'he's not sane,' inappropriate as it may have been for a machine. "He's a bigger threat to them than to us."_

_"How long will it take for the scans to be completed?"_

_Neo could not remember the name of the woman who addressed him. He answered quickly. "Between twenty and thirty days."_

_It seemed like a very long time. He had to remind himself that he'd already agreed to do this, that it was not worth jeopardizing the truce when 01 was asking them for help—and they were asking. They were desperate, easy as it would have been to claim they were lying. He wanted to say 'wait,' say, 'I don't know.' The only way to check the impulse was with the knowledge that he would be on the ship too—he would be there to stop it if something went wrong. And even that assertion felt hollow. The discussion moved on, and he didn't say anything else at all._

_"The operation is approved. Your ship will leave within the next three days. You are expected to have radio contact with the city at all times, and to stay clear of broadcast depth after the first four…"_

_She was addressing Morpheus and Locke now, more than anyone else. The decision was made. He relaxed because the decision was made._

*

"You're on board one of our ships. Your system has handed you over to us, and as of this moment you are our prisoner."

Locke pauses, leaving all implications unspoken. Neo can't help but wonder, from his own corner of the room, if Locke isn't being intentionally sadistic. It doesn't matter. No one cares to stop him. Just this once he's found a target who may well deserve worse than he can do.

They're all waiting for him to continue, and it comes as a jolt to everyone present when Smith gets there first. He asks, simply, "Then why haven't you killed me?"

The question is delivered with remarkable calm, all things considered, blank and contemptuous, and for the first time all morning Locke seems taken off his guard, "We intend to. Scans are being run on the Matrix as we speak."

He stops. He could have been clearer, but Smith seems to understand, and he doesn't protest. Neo catches a shade of something in his expression, but, on the whole, he accepts the news with an indifference that's oddly disconcerting, if not wholly out of character. It's hard not to wonder what went on with him over the course of the past three months. There isn't time to make many guesses.

Neo finds it hard to tell, at first, if Smith had genuinely blacked out, or if he'd simply decided to ignore them, but once a few seconds have passed he takes his cue to come forward. The trick of the shadows worked surprisingly well—Smith never saw him. The others are still exchanging glances when he stops to stand beside Morpheus, speaking quietly. "That went well…" The sarcasm comes across more grimly than he'd have liked.

Everyone comes back to life at once. Locke takes a few steps away from the jack-in chair, looking, if anything, faintly shaken and says, "Get him locked up."

Link is the first to react. "Yes, sir." He hesitates for a beat but once he's gone on Locke turns and strides out of the room, presumably to radio home. Compared to expectations, it did go well. It really did.

And then— "Christ! It's like a funeral march up here. Did it work?" A resounding clang makes them all jump, and they turn to see Gage coming up the hatch. Morpheus gives him a flat nod.

"Yes, it worked."

"Well, that's good. Engine's alright, if you wanted to know."

"Thank you, Gage."

The younger man throws a glance around the room, absently wiping grease off his hands, "Yeah, no problem. So, what'd I miss?"

Neo turns, then, and takes the opportunity to slip out of the room. He won't be needed for a while, he decides. They are done. It might have been better to give an explanation, but he'd never have gotten away, and he needs time to think. There's been precious little of that over the last few days.

Gage sees him, and comments as he'd known he would, but he can only catch the first word or two before he steps into the hall. The walls are heavy iron. Sound doesn't make it through once the door is pulled shut. He's alone and he can hear his footsteps echoing from ceiling to floor. Beyond that, it's silent.


End file.
